I had to clean my ducklings every day. They are very very VERY messy. I am going to assume you have a water container that you would use for chicks. The ducks typically splash around in that, soak all the bedding, and then poop on top of all that. Get a water bottle designed for rabbits or guinea pigs with the metal nipple that hangs down. The ducks are incapable of splashing in it and it keeps the litter much cleaner. Ducks require much more cleaning than chickens however. They don't scratch the ground which helps in churning the clean litter underneath, they simply pack it down. Ducklings do not need a place to swim until they have feathers but they do occasionally need to dunk their bills underwater. I would give them a little bowl of water for a few minutes before cleaning time.

Keeping the bedding dry is a good first step. I had to clean the brooder three to five times a day for my eleven runners, as I did not have an optimal setup for the water.

Containing the splash is the best way I have found to avoid problems. Something with high sides and a bottom that has a few inches of space in it to hold sawdust that can absorb water works very nicely, too.

Ducklings need to be able to wash their heads regularly to avoid serious eye, sinus and ear infections.